In the present work, a comparison study of the Ni catalysts supported on SBA-15 silica support prepared with and without the addition of organic ligands (citric acid and ethylenediaminetetraacetic acid (EDTA) was undertaken. The aim of this study was to inquire on the effect of the addition of organic ligands on the characteristics of the supported NiO and Ni nanoparticles and on their activity and selectivity in hydrogenation (HYD) of aromatics. Catalysts with different metal loadings (5, 10 and 20 wt. % of Ni) were prepared, characterized by nitrogen physisorption, small-angle and powder XRD, TPR, UV-vis DRS, and HRTEM, and tested in HYD of naphthalene (NP). It was found that Ni(II)-Ligand complexes were formed in aqueous solutions of Ni(NO3)2 containing citric acid (CA) or EDTA. Catalysts prepared from impregnation solutions with and without ligands had different textural characteristics and dispersion of NiO particles after calcination at 500 °C for 4 h. As it was shown by XRD, DRS and TPR, dispersion of NiO particles significantly increased when EDTA was used, whereas it noticeably decreased after the addition of CA. Similar trends were observed in the dispersion of metallic Ni particles after reduction of the NiO/SBA-15 precursors (HRTEM). In line with the characterization results, catalytic activity tests revealed strong differences in the activity of the prepared Ni/SBA-15 catalysts in hydrogenation of naphthalene. Catalysts prepared with the addition of EDTA were more active than those prepared without ligands. On the contrary, the HYD activity of a series of the Ni catalysts prepared with citric acid was lower than of other corresponding samples. The reasons of such a different behavior of the catalysts prepared with two organic ligands used are discussed on the basis of the obtained characterization results.